def testAllStrainHetero(self):
"""Verify computation of strain heterogeneity score on highly similar sequences."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.95], 'g3': [0.95]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 100.0)
def testMixedStrainHetero(self):
"""Verify computation of strain heterogeneity score on sequences with variable similarity."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.1], 'g3': [0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 0.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 1.0 * 100 / 3.0)
def testAllStrainHetero(self):
"""Verify computation of strain heterogeneity score on highly similar sequences."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.95], 'g3': [0.95]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 100.0)
def testMultiCopyStrainHetero(self):
"""Verify computation of strain heterogeneity score when there are multiple copies of a sequence."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95, 0.95, 0.95], 'g2': [0.1, 0.1, 0.1], 'g3': [0.95, 0.1, 0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0 / 3.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 4.0 * 100 / 9.0)
def testMixedStrainHetero(self):
"""Verify computation of strain heterogeneity score on sequences with variable similarity."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {'g1': [0.95], 'g2': [0.1], 'g3': [0.1]}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 0.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 1.0 * 100 / 3.0)
def testMultiCopyStrainHetero(self):
"""Verify computation of strain heterogeneity score when there are multiple copies of a sequence."""
aai = AminoAcidIdentity()
aaiScores = defaultdict(dict)
aaiScores['b1'] = {
'g1': [0.95, 0.95, 0.95],
'g2': [0.1, 0.1, 0.1],
'g3': [0.95, 0.1, 0.1]
}
aaiHetero, aaiMeanBinHetero = aai.strainHetero(aaiScores, 0.9)
self.assertAlmostEqual(aaiHetero['b1']['g1'], 1.0)
self.assertAlmostEqual(aaiHetero['b1']['g2'], 0.0)
self.assertAlmostEqual(aaiHetero['b1']['g3'], 1.0 / 3.0)
self.assertAlmostEqual(aaiMeanBinHetero['b1'], 4.0 * 100 / 9.0)